genome.fa.s4.2.7.7.80.10.50.1000.122.html

Tandem Repeats Finder Program written by:

Gary Benson
Program in Bioinformatics
Boston University
Version 4.09

Please cite:
G. Benson,
"Tandem repeats finder: a program to analyze DNA sequences"
Nucleic Acid Research(1999)
Vol. 27, No. 2, pp. 573-580.

Sequence: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Length:  62178258

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190   191   192   
          193   194   195   196   197   198   

This is table  122  of  198  ( 23681 repeats found )

Click on indices to view alignment

Table Explanation

Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39265823--39266137	147	2.1	148	81	4	368	30	16	21	30	1.96
39268006--39268045	13	3.0	13	83	16	55	30	2	2	65	1.19
39268190--39268235	3	15.3	3	100	0	92	32	0	0	67	0.91
39268288--39268349	22	2.9	21	83	11	72	37	1	3	58	1.24
39268411--39268532	22	5.9	20	73	8	77	40	4	0	53	1.28
39268435--39268639	2	104.0	2	72	8	116	43	7	1	46	1.41
39274410--39274470	2	30.5	2	96	0	113	49	1	0	49	1.10
39274578--39274609	12	2.7	12	95	0	55	18	9	0	71	1.12
39277216--39277248	12	2.8	12	90	4	50	42	33	18	6	1.75
39278282--39278334	21	2.5	21	93	0	88	30	37	9	22	1.86
39279486--39279553	23	2.8	24	88	11	102	42	10	0	47	1.37
39279597--39279688	27	3.4	27	85	5	116	25	28	27	19	1.99
39279771--39279810	11	3.7	11	83	6	55	72	0	27	0	0.85
39279771--39279804	10	3.4	10	92	8	52	73	0	26	0	0.83
39279918--39279955	3	12.3	3	88	5	58	31	0	5	63	1.17
39279954--39279997	3	14.7	3	100	0	88	0	0	31	68	0.90
39280183--39280235	26	2.0	26	96	0	97	43	0	7	49	1.31
39280241--39280271	12	2.6	12	94	0	53	19	0	19	61	1.35
39280181--39280280	26	4.0	25	65	16	73	34	0	12	54	1.38
39280821--39280865	18	2.5	18	81	0	63	28	8	48	13	1.72
39283058--39283119	27	2.3	26	79	17	65	1	27	0	70	0.96
39283089--39283164	22	3.8	21	72	22	65	1	28	0	69	0.96
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39283078--39283164	38	2.4	35	83	12	120	1	28	0	70	0.95
39283055--39283159	17	6.2	16	70	18	54	0	28	0	70	0.94
39283057--39283162	16	6.1	17	69	24	71	0	28	0	70	0.93
39283421--39283488	25	2.6	25	90	9	102	48	0	10	41	1.37
39284496--39284535	2	20.0	2	100	0	80	50	0	0	50	1.00
39284728--39284804	32	2.4	34	87	12	96	37	0	10	51	1.36
39292603--39292632	2	15.0	2	92	0	51	46	3	0	50	1.18
39292647--39292792	53	2.7	55	87	7	199	43	14	8	33	1.75
39294578--39294633	23	2.4	23	78	0	58	42	25	14	17	1.87
39305587--39305635	25	2.0	25	83	0	62	34	14	12	38	1.83
39315189--39315315	35	3.6	35	87	3	175	16	11	31	40	1.83
39317107--39317148	21	2.0	22	85	4	59	38	23	4	33	1.76
39319222--39319340	42	2.8	40	82	10	134	30	26	17	26	1.97
39322914--39323015	50	2.0	50	100	0	186	46	17	13	22	1.83
39329216--39329418	40	5.1	40	87	1	284	43	28	15	12	1.83
39329228--39329418	80	2.4	80	94	0	328	43	27	15	13	1.84
39345301--39345327	6	4.5	6	100	0	54	14	0	0	85	0.61
39346753--39346783	9	3.4	9	90	0	53	25	12	22	38	1.90
39346838--39346874	9	4.1	9	85	0	56	48	13	8	29	1.71
39349704--39349839	6	22.7	6	98	0	263	16	0	33	50	1.51
39357793--39357893	33	3.4	32	70	30	105	44	16	7	30	1.77
39357749--39357904	56	2.8	56	92	3	269	44	17	8	30	1.78
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39359602--39359638	2	19.0	2	94	5	67	51	0	0	48	1.00
39362228--39362356	43	3.0	43	77	6	145	22	17	28	31	1.96
39379303--39379423	63	1.9	64	81	5	147	29	27	18	24	1.98
39388836--39389114	28	9.8	27	79	10	218	57	7	12	22	1.60
39388831--39389114	57	4.9	57	78	6	259	56	7	13	23	1.62
39391586--39391653	21	3.0	23	71	20	72	27	17	1	52	1.53
39392156--39392206	17	2.8	19	82	11	70	56	5	5	31	1.47
39396706--39396860	79	2.0	79	86	0	220	29	12	14	43	1.81
39401781--39401816	8	4.5	8	100	0	72	13	0	22	63	1.29
39412688--39412988	67	4.5	67	90	1	489	55	6	12	25	1.61
39412688--39412988	132	2.3	133	92	2	507	55	6	12	25	1.61
39417804--39417865	29	2.1	29	82	5	72	43	8	0	48	1.32
39421948--39421991	16	2.8	16	96	0	79	38	0	34	27	1.57
39421970--39422079	45	2.6	43	80	9	129	33	5	29	31	1.80
39422201--39422255	25	2.2	25	84	9	69	52	1	0	45	1.11
39422190--39422263	24	3.0	25	78	13	73	52	2	0	44	1.15
39422223--39422269	23	2.0	25	83	8	62	59	0	0	40	0.97
39424813--39424845	16	2.1	16	94	0	57	63	15	15	6	1.49
39428937--39428962	4	6.5	4	100	0	52	76	0	0	23	0.78
39434980--39435013	3	11.3	3	87	0	50	32	41	0	26	1.56
39448984--39449018	18	2.0	18	88	5	54	45	0	2	51	1.16
39451703--39451762	27	2.2	27	100	0	120	35	16	21	26	1.95
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39452066--39452261	92	2.1	91	82	2	232	31	6	6	55	1.50
39452256--39452294	19	2.0	20	90	5	62	30	10	5	53	1.56
39452282--39452325	21	2.1	21	95	0	79	31	11	0	56	1.35
39454184--39454214	16	1.9	16	100	0	62	22	0	0	77	0.77
39461867--39461901	17	2.1	17	88	0	52	68	2	0	28	1.04
39469711--39470255	84	6.6	83	74	13	421	44	12	11	31	1.77
39469861--39469885	5	5.0	5	100	0	50	80	0	0	20	0.72
39469779--39470347	86	6.7	87	77	11	524	43	12	11	32	1.78
39469724--39470255	248	2.1	249	89	2	800	44	12	11	31	1.78
39470309--39470505	79	2.5	79	83	3	261	38	11	18	31	1.87
39474844--39475231	109	3.6	109	88	4	563	25	0	14	60	1.38
39475122--39475326	97	2.1	95	86	4	286	27	0	13	58	1.39
39475551--39475613	21	2.9	22	77	11	58	30	6	6	57	1.49
39476595--39476681	33	2.6	33	79	0	111	21	48	10	19	1.79
39480753--39480801	25	1.9	26	84	12	66	59	10	2	28	1.41
39480543--39480809	115	2.4	106	79	13	324	56	14	1	26	1.48
39480785--39480830	11	4.3	11	81	15	51	67	8	0	23	1.18
39481029--39481107	27	2.9	27	79	7	88	22	26	26	24	2.00
39481289--39481344	29	1.9	29	96	0	103	30	23	7	39	1.81
39484450--39484534	46	1.9	45	83	7	111	36	27	12	23	1.91
39484540--39484730	51	3.8	51	80	8	228	30	28	17	24	1.97
39484538--39484722	101	1.8	102	89	3	293	30	27	17	23	1.97
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39495018--39495052	3	11.7	3	93	0	61	37	0	0	62	0.95
39495003--39495055	6	8.8	6	93	0	52	47	0	0	52	1.00
39494999--39495062	9	7.1	9	90	0	56	50	0	0	50	1.00
39495849--39495887	21	1.9	20	85	15	53	74	5	15	5	1.17
39499307--39499435	34	3.8	34	86	0	168	27	14	14	42	1.85
39499307--39499435	68	1.9	68	90	0	204	27	14	14	42	1.85
39500967--39501069	45	2.3	43	80	9	116	26	18	16	38	1.92
39500983--39501072	45	2.0	45	86	0	126	27	18	15	37	1.92
39508074--39508120	19	2.5	19	89	6	69	34	0	8	57	1.29
39509197--39509233	19	1.9	19	94	0	65	13	10	10	64	1.49
39516738--39516789	24	2.2	24	85	0	68	51	7	3	36	1.49
39520671--39520796	43	2.9	41	80	12	137	19	19	29	31	1.96
39521634--39521900	47	5.7	47	96	0	471	24	17	15	42	1.88
39521634--39521942	47	6.6	47	92	0	429	25	18	15	40	1.90
39521909--39521959	23	2.2	23	89	0	75	23	17	17	41	1.90
39521917--39521968	23	2.3	23	86	0	68	28	17	13	40	1.87
39522611--39522677	9	7.4	9	89	0	89	25	7	22	44	1.78
39522841--39522865	12	2.1	12	100	0	50	16	24	36	24	1.94
39522983--39523015	2	16.5	2	100	0	66	48	0	0	51	1.00
39525127--39525178	24	2.2	24	89	0	77	50	9	3	36	1.54
39528788--39528863	40	1.9	40	81	10	93	23	26	28	21	1.99
39529008--39529073	22	3.0	21	74	14	62	27	25	0	46	1.53
Indices	Period Size	Copy Number	Consensus Size	Percent Matches	Percent Indels	Score	A	C	G	T	Entropy (0-2)
39529032--39529063	11	2.9	11	100	0	64	28	34	0	37	1.57
39530747--39530814	30	2.3	30	76	0	73	35	44	8	11	1.72
39533763--39533819	25	2.3	25	84	0	69	40	12	5	42	1.65
39533868--39533917	20	2.5	19	80	6	55	34	24	8	34	1.84
39534066--39534157	23	3.9	23	78	15	98	31	20	25	22	1.98
39537074--39537364	126	2.3	126	93	0	501	26	21	20	31	1.98
39537397--39537677	97	2.9	95	79	10	322	41	17	3	37	1.67
39538993--39539027	16	2.2	17	90	10	56	85	0	14	0	0.59
39538993--39539027	17	2.1	16	89	5	52	85	0	14	0	0.59
39540535--39540588	25	2.2	24	87	9	74	66	1	0	31	1.02

Tables:   1   2   3   4   5   6   7   8   9   10   11   12   13   14   15   16   
          17   18   19   20   21   22   23   24   25   26   27   28   29   30   31   32   
          33   34   35   36   37   38   39   40   41   42   43   44   45   46   47   48   
          49   50   51   52   53   54   55   56   57   58   59   60   61   62   63   64   
          65   66   67   68   69   70   71   72   73   74   75   76   77   78   79   80   
          81   82   83   84   85   86   87   88   89   90   91   92   93   94   95   96   
          97   98   99   100   101   102   103   104   105   106   107   108   109   110   111   112   
          113   114   115   116   117   118   119   120   121   122   123   124   125   126   127   128   
          129   130   131   132   133   134   135   136   137   138   139   140   141   142   143   144   
          145   146   147   148   149   150   151   152   153   154   155   156   157   158   159   160   
          161   162   163   164   165   166   167   168   169   170   171   172   173   174   175   176   
          177   178   179   180   181   182   183   184   185   186   187   188   189   190   191   192   
          193   194   195   196   197   198